Odd issue - Gamecube Controllers won't respond

[Spongejordan123]

I originally started on Smashboards, but it's apparent they have no idea what they're doing :P

The situation -
I used to play Brawl+ and other modifications to it just fine via Gecko 1.9.3. I changed the codes I was using around, and all the sudden, Gecko no longer allowed my Gamecube Controllers to play Brawl, regardless if there were codes or not. Meaning, I have a near-blank SD Card with ONLY Gecko on it. The Gamecube Controller can be used to navigate in Homebrew Channel as well as Gecko itself, however it completely stops working after Brawl loads. So, I tried my Backup Loader, didn't work. However, they work absolutely fine in the Disc Channel. I was really confused, so I thought maybe my disc was too scratched to play with modifications.

So I got a friend's Brawl disc. Same issue. Got a different SD Card. Same issue.

At this point, the only thing constant was the Wii (I used different Gecko 1.9's back when I first got the error) However, I don't understand how it COULD be the Wii itself.

Anyone have any suggestions on how to fix it?

*edit* Also, I'm running System Menu 4.1.

*edit 2* Oddly enough, rebooting and loading through the Disc Channel makes the codes work, however the rebooter reboots regardless if the DVD is successfully read or not, which is no bueno. I just wish plain-ol'-Gecko worked.